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2022 Journal Article Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and BokMacDonald, Michael A., Barry, Craig, Groves, Teddy, Martínez, Verónica S., Gray, Peter P., Baker, Kym, Shave, Evan, Mahler, Stephen, Munro, Trent, Marcellin, Esteban and Nielsen, Lars K. (2022). Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and Bok. Biotechnology and Bioengineering, 119 (6), 1380-1391. doi: 10.1002/bit.28062 |
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2022 Journal Article Soft‐sensors application for automated feeding control in high‐throughput mammalian cell culturesMartínez‐Monge, I., Martínez, C., Decker, M., Udugama, I. A., Marín de Mas, I., Gernaey, K. V. and Nielsen, L.K. (2022). Soft‐sensors application for automated feeding control in high‐throughput mammalian cell cultures. Biotechnology and Bioengineering, 119 (4), 1077-1090. doi: 10.1002/bit.28032 |
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2022 Journal Article Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potentialBarry, Craig P., Gillane, Rosemary, Talbo, Gert H., Plan, Manual, Palfreyman, Robin, Haber-Stuk, Andrea K., Power, John, Nielsen, Lars K. and Marcellin, Esteban (2022). Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Molecular Omics, 18 (3), 226-236. doi: 10.1039/d1mo00150g |
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2021 Journal Article Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural networkGrapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7 |
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2021 Journal Article Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putidaKozaeva, Ekaterina, Volkova, Svetlana, Matos, Marta R.A., Mezzina, Mariela P., Wulff, Tune, Volke, Daniel C., Nielsen, Lars K. and Nikel, Pablo I. (2021). Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida. Metabolic Engineering, 67, 373-386. doi: 10.1016/j.ymben.2021.07.014 |
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2021 Journal Article Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, AustraliaPetersen, Ian, Paungfoo-Lonhienne, Chanyarat, Marcellin, Esteban, Nielsen, Lars Keld and Gonzalez, Axayacatl (2021). Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, Australia. Fermentation, 7 (2) 58, 1-17. doi: 10.3390/fermentation7020058 |
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2021 Journal Article multiTFA: a Python package for multi-variate thermodynamics-based flux analysisMahamkali, Vishnuvardhan, McCubbin, Tim, Beber, Moritz Emanuel, Noor, Elad, Marcellin, Esteban and Nielsen, Lars Keld (2021). multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. Bioinformatics, 37 (18), 3064-3066. doi: 10.1093/bioinformatics/btab151 |
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2021 Journal Article Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationshipsSchwaber, Jessica L., Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K., Trau, Matt and Nielsen, Lars K. (2021). Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS ONE, 16 (2 ) e0246107, e0246107. doi: 10.1371/journal.pone.0246107 |
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2021 Book Chapter Metabolic modeling and omics data integration: a systems biology approach to food sciencede Mas, Igor Marin, de Leeuw, Marina, Ghaffari, Pouyan and Nielsen, Lars K. (2021). Metabolic modeling and omics data integration: a systems biology approach to food science. Comprehensive foodomics. (pp. 396-417) edited by Alejandro Cifuentes. Amsterdam, Netherlands: Elsevier. doi: 10.1016/B978-0-08-100596-5.22914-4 |
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2021 Journal Article Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applicationsMacDonald, Michael A., Nöbel, Matthias, Roche Recinos, Dinora, Martínez, Verónica S., Schulz, Benjamin L., Howard, Christopher B., Baker, Kym, Shave, Evan, Lee, Yih Yean, Marcellin, Esteban, Mahler, Stephen, Nielsen, Lars Keld and Munro, Trent (2021). Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications. Critical Reviews in Biotechnology, 42 (7), 1-17. doi: 10.1080/07388551.2021.1998821 |
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2020 Journal Article SmartPeak automates targeted and quantitative metabolomics data processingKutuzova, Svetlana, Colaianni, Pasquale, Röst, Hannes, Sachsenberg, Timo, Alka, Oliver, Kohlbacher, Oliver, Burla, Bo, Torta, Federico, Schrübbers, Lars, Kristensen, Mette, Nielsen, Lars, Herrgård, Markus J. and McCloskey, Douglas (2020). SmartPeak automates targeted and quantitative metabolomics data processing. Analytical Chemistry, 92 (24), 15968-15974. doi: 10.1021/acs.analchem.0c03421 |
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2020 Journal Article Time-course transcriptomics reveals that amino acids catabolism plays a key role in toxinogenesis and morphology in Clostridium tetaniOrellana, Camila A., Zaragoza, Nicolas E., Licona-Cassani, Cuauhtemoc, Palfreyman, Robin W., Cowie, Nicholas, Moonen, Glenn, Moutafis, George, Power, John, Nielsen, Lars K. and Marcellin, Esteban (2020). Time-course transcriptomics reveals that amino acids catabolism plays a key role in toxinogenesis and morphology in Clostridium tetani. Journal of Industrial Microbiology and Biotechnology, 47 (12), 1059-1073. doi: 10.1007/s10295-020-02330-3 |
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2020 Conference Publication Revamping the model CO-fermenting acetogen, Clostridium autoethanogenum, as a CO2-valorisation platformHeffernan, James, Valgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Casini, Isabella, Plan, Manuel, Tappel, Ryan, Simpson, Sean D., Köpke, Michael, Gonzalez-Garcia, Ricardo A., Nielsen, Lars K. and Marcellin, Esteban (2020). Revamping the model CO-fermenting acetogen, Clostridium autoethanogenum, as a CO2-valorisation platform. International Chain Elongation Conference 2020, Virtual, 26-27 October 2020. Wageningen, Germany: Wageningen University and Research. doi: 10.18174/icec2020.18019 |
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2020 Journal Article A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversityMcCubbin, Tim, Gonzalez-Garcia, R. Axayacatl, Palfreyman, Robin W., Stowers, Chris, Nielsen, Lars K. and Marcellin, Esteban (2020). A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversity. Genes, 11 (10) 1115, 1-26. doi: 10.3390/genes11101115 |
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2020 Journal Article Multicopy targeted Integration for accelerated development of high-producing Chinese hamster ovary cellsSergeeva, Daria, Lee, Gyun Min, Nielsen, Lars Keld and Grav, Lise Marie (2020). Multicopy targeted Integration for accelerated development of high-producing Chinese hamster ovary cells. ACS Synthetic Biology, 9 (9) acssynbio.0c00322, 2546-2561. doi: 10.1021/acssynbio.0c00322 |
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2020 Journal Article What CHO is made of: variations in the biomass composition of Chinese hamster ovary cell linesSzéliová, Diana, Ruckerbauer, David E., Galleguillos, Sarah N., Petersen, Lars B., Natter, Klaus, Hanscho, Michael, Troyer, Christina, Causon, Tim, Schoeny, Harald, Christensen, Hanne B., Lee, Dong-Yup, Lewis, Nathan E., Koellensperger, Gunda, Hann, Stephan, Nielsen, Lars K., Borth, Nicole and Zanghellini, Jürgen (2020). What CHO is made of: variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic Engineering, 61, 288-300. doi: 10.1016/j.ymben.2020.06.002 |
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2020 Journal Article ‘Omics driven discoveries of gene targets for apoptosis attenuation in CHO cellsOrellana, Camila A., Martínez, Verónica S., MacDonald, Michael A., Henry, Matthew N., Gillard, Marianne, Gray, Peter P., Nielsen, Lars K., Mahler, Stephen and Marcellin, Esteban (2020). ‘Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells. Biotechnology and Bioengineering, 118 (1) bit.27548, 481-490. doi: 10.1002/bit.27548 |
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2020 Journal Article Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenumMahamkali, Vishnuvardhan, Valgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Plan, Manuel, Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2020). Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proceedings of the National Academy of Sciences of the United States of America, 117 (23), 13168-13175. doi: 10.1073/pnas.1919531117 |
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2020 Journal Article Heterologous production of 6-deoxyerythronolide B in Escherichia coli through the wood werkman cycleGonzalez-Garcia, R. Axayacatl, Nielsen, Lars K. and Marcellin, Esteban (2020). Heterologous production of 6-deoxyerythronolide B in Escherichia coli through the wood werkman cycle. Metabolites, 10 (6) 228, 228. doi: 10.3390/metabo10060228 |
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2020 Journal Article Correction to: Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production (Applied Microbiology and Biotechnology, (2016), 100, 21, (9229-9237), 10.1007/s00253-016-7811-2)Tierrafría, Víctor H., Licona-Cassani, Cuauhtemoc, Maldonado-Carmona, Nidia, Romero-Rodríguez, Alba, Centeno-Leija, Sara, Marcellin, Esteban, Rodríguez-Sanoja, Romina, Ruiz-Villafán, Beatriz, Nielsen, Lars K. and Sánchez, Sergio (2020). Correction to: Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production (Applied Microbiology and Biotechnology, (2016), 100, 21, (9229-9237), 10.1007/s00253-016-7811-2). Applied Microbiology and Biotechnology, 104 (8), 3687-3687. doi: 10.1007/s00253-020-10499-x |
